Skip to main content
Log in

Microenzymes: Is There Anybody Out There?

  • Published:
The Protein Journal Aims and scope Submit manuscript

Abstract

Biological macromolecules are found in different shapes and sizes. Among these, enzymes catalyze biochemical reactions and are essential in all organisms, but is there a limit size for them to function properly? Large enzymes such as catalases have hundreds of kDa and are formed by multiple subunits, whereas most enzymes are smaller, with molecular weights of 20–60 kDa. Enzymes smaller than 10 kDa could be called microenzymes and the present literature review brings together evidence of their occurrence in nature. Additionally, bioactive peptides could be a natural source for novel microenzymes hidden in larger peptides and molecular downsizing could be useful to engineer artificial enzymes with low molecular weight improving their stability and heterologous expression. An integrative approach is crucial to discover and determine the amino acid sequences of novel microenzymes, together with their genomic identification and their biochemical biological and evolutionary functions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

Data Availability

All data generated or analyzed during this study are included in this published article.

Code Availability

Not Applicable.

References

  1. Krüger M, Linke WA (2011) The giant protein titin: a regulatory node that integrates myocyte signaling pathways. J Biol Chem 286:9905–9912. https://doi.org/10.1074/jbc.R110.173260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Moss GP, Smith PaS, Tavernier D (1995) Glossary of class names of organic compounds and reactivity intermediates based on structure (IUPAC recommendations 1995). Pure Appl Chem 67:1307–1375. https://doi.org/10.1351/pac199567081307

    Article  Google Scholar 

  3. Kulberg A, Petyaev IM, Zamotaeva NG (1988) Catalytic properties and catalytic destruction of cellular receptors (R-proteins). Immunology 3:37–40

    Google Scholar 

  4. Robinson PK (2015) Enzymes: principles and biotechnological applications. Essays Biochem 59:1–41. https://doi.org/10.1042/bse0590001

    Article  PubMed  PubMed Central  Google Scholar 

  5. Tolmacheva AS, Nevinsky GA (2022) Essential protective role of catalytically active antibodies (Abzymes) with Redox antioxidant functions in animals and humans. Int J Mol Sci 23:3898. https://doi.org/10.3390/ijms23073898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Nagel B, Dellweg H, Gierasch LM (1992) Glossary for chemists of terms used in biotechnology (IUPAC recommendations 1992). Pure Appl Chem 64:143–168. https://doi.org/10.1351/pac199264010143

    Article  CAS  Google Scholar 

  7. McDonald AG, Tipton KF (2023) Enzyme nomenclature and classification: the state of the art. FEBS J 290:2214–2231. https://doi.org/10.1111/febs.16274

    Article  CAS  PubMed  Google Scholar 

  8. Drula E, Garron M-L, Dogan S et al (2022) The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res 50:D571–D577. https://doi.org/10.1093/nar/gkab1045

    Article  CAS  PubMed  Google Scholar 

  9. Alfonso-Prieto M, Biarnés X, Vidossich P, Rovira C (2009) The molecular mechanism of the catalase reaction. J Am Chem Soc 131:11751–11761. https://doi.org/10.1021/ja9018572

    Article  CAS  PubMed  Google Scholar 

  10. Glorieux C, Calderon PB (2017) Catalase, a remarkable enzyme: targeting the oldest antioxidant enzyme to find a new cancer treatment approach. Biol Chem 398:1095–1108. https://doi.org/10.1515/hsz-2017-0131

    Article  CAS  PubMed  Google Scholar 

  11. Sioud M, Opstad A, Hendry P et al (1997) A minimised hammerhead ribozyme with activity against interleukin-2 in human cells. Biochem Biophys Res Commun 231:397–402. https://doi.org/10.1006/bbrc.1997.6099

    Article  CAS  PubMed  Google Scholar 

  12. Schenk RU, Bjorksten J (1973) Search for microenzymes-enzyme of Bacillus cereus. Finska Kemistsamfundets Meddelanden 82:26–46

    CAS  Google Scholar 

  13. Basrai MA, Hieter P, Boeke JD (1997) Small open reading frames: beautiful needles in the haystack. Genome Res 7:768–771. https://doi.org/10.1101/gr.7.8.768

    Article  CAS  PubMed  Google Scholar 

  14. Chen J, Brunner A-D, Cogan JZ et al (2020) Pervasive functional translation of noncanonical human open reading frames. Science 367:1140–1146. https://doi.org/10.1126/science.aay0262

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  15. Couso J-P, Patraquim P (2017) Classification and function of small open reading frames. Nat Rev Mol Cell Biol 18:575–589. https://doi.org/10.1038/nrm.2017.58

    Article  CAS  PubMed  Google Scholar 

  16. Tiessen A, Pérez-Rodríguez P, Delaye-Arredondo LJ (2012) Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes. BMC Res Notes 5:1–23. https://doi.org/10.1186/1756-0500-5-85

    Article  CAS  Google Scholar 

  17. Ruiz-Orera J, Albà MM (2019) Translation of small open reading frames: roles in regulation and evolutionary innovation. Trends Genet 35:186–198. https://doi.org/10.1016/j.tig.2018.12.003

    Article  CAS  PubMed  Google Scholar 

  18. Makarewich CA, Olson EN (2017) Mining for micropeptides. Trends Cell Biol 27:685–696. https://doi.org/10.1016/j.tcb.2017.04.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Vaux DL, Korsmeyer SJ (1999) Cell death in development. Cell 96:245–254. https://doi.org/10.1016/S0092-8674(00)80564-4

    Article  CAS  PubMed  Google Scholar 

  20. Saghatelian A, Couso JP (2015) Discovery and characterization of smORF-encoded bioactive polypeptides. Nat Chem Biol 11:909–916. https://doi.org/10.1038/nchembio.1964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Itoh K, Nakamura K, Iijima M, Sesaki H (2013) Mitochondrial dynamics in neurodegeneration. Trends Cell Biol 23:64–71. https://doi.org/10.1016/j.tcb.2012.10.006

    Article  CAS  PubMed  Google Scholar 

  22. Tharakan R, Sawa A (2021) Minireview: novel micropeptide discovery by proteomics and deep sequencing methods. Front Genet 12:651485. https://doi.org/10.3389/fgene.2021.651485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lluch-Senar M, Delgado J, Chen W-H et al (2015) Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Mol Syst Biol 11:780. https://doi.org/10.15252/msb.20145558

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. VanOrsdel CE, Kelly JP, Burke BN et al (2018) Identifying new small proteins in Escherichia coli. Proteomics 18:1700064. https://doi.org/10.1002/pmic.201700064

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kastenmayer JP, Ni L, Chu A et al (2006) Functional genomics of genes with small open reading frames (sORFs) in S. Cerevisiae. Genome Res 16:365–373. https://doi.org/10.1101/gr.4355406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Delcourt V, Staskevicius A, Salzet M et al (2018) Small proteins encoded by unannotated ORFs are rising stars of the proteome, confirming shortcomings in genome annotations and current vision of an mRNA. Proteomics 18:e1700058. https://doi.org/10.1002/pmic.201700058

    Article  CAS  PubMed  Google Scholar 

  27. Murgoci A-N, Cardon T, Aboulouard S et al (2020) Reference and ghost proteins identification in rat C6 glioma extracellular vesicles. iScience 23:101045. https://doi.org/10.1016/j.isci.2020.101045

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  28. Jeffery CJ (2018) Protein moonlighting: what is it, and why is it important? Philos Trans R Soc Lond B Biol Sci 373:20160523. https://doi.org/10.1098/rstb.2016.0523

    Article  CAS  PubMed  Google Scholar 

  29. Mani M, Chen C, Amblee V et al (2015) MoonProt: a database for proteins that are known to moonlight. Nucleic Acids Res 43:D277–282. https://doi.org/10.1093/nar/gku954

    Article  CAS  PubMed  Google Scholar 

  30. Jeffery CJ (2020) Enzymes, pseudoenzymes, and moonlighting proteins: diversity of function in protein superfamilies. FEBS J 287:4141–4149. https://doi.org/10.1111/febs.15446

    Article  CAS  PubMed  Google Scholar 

  31. Chen LH, Kenyon GL, Curtin F et al (1992) 4-Oxalocrotonate tautomerase, an enzyme composed of 62 amino acid residues per monomer. J Biol Chem 267:17716–17721

    Article  CAS  PubMed  Google Scholar 

  32. Poddar H, Rahimi M, Geertsema EM et al (2015) Evidence for the formation of an enamine species during Aldol and Michael-type addition reactions promiscuously catalyzed by 4-Oxalocrotonate tautomerase. ChemBioChem 16:738–741. https://doi.org/10.1002/cbic.201402687

    Article  CAS  PubMed  Google Scholar 

  33. Whitman CP (2002) The 4-oxalocrotonate tautomerase family of enzymes: how nature makes new enzymes using a β–α–β structural motif. Arch Biochem Biophys 402:1–13. https://doi.org/10.1016/S0003-9861(02)00052-8

    Article  CAS  PubMed  Google Scholar 

  34. Adoga G, Mattey M (1979) Properties of an extracellular peptide with esterase activity produced by Candida lipolytica. FEMS Microbiol Lett 6:61–63. https://doi.org/10.1111/j.1574-6968.1979.tb04278.x

    Article  CAS  Google Scholar 

  35. Laxer S, Pnsky A, Bartoov B (1981) Further purification and characterization of a thermophilic rennet. Biotechnol Bioeng 23:2483–2492. https://doi.org/10.1002/bit.260231108

    Article  CAS  Google Scholar 

  36. Guagliardi A, Cerchia L, De Rosa M et al (1992) Isolation of a thermostable enzyme catalyzing disulfide bond formation from the archaebacterium Sulfolobus solfataricus. FEBS Lett 303:27–30. https://doi.org/10.1016/0014-5793(92)80470-2

    Article  CAS  PubMed  Google Scholar 

  37. Steele DB, Fiske MJ, Steele BP, Kelley VC (1992) Production of a low-molecular-weight, alkaline-active, thermostable protease by a novel, spiral-shaped bacterium, Kurthia spiroforme, sp. nov. Enzym Microb Technol 14:358–360. https://doi.org/10.1016/0141-0229(92)90003-7

    Article  CAS  Google Scholar 

  38. Simões D, de CM, McNeill D, Kristiansen B, Mattey M (1995) Extracellular esterase activity from Bacillus stearothermophilus. Biotechnol Lett 17:953–958. https://doi.org/10.1007/BF00127433

    Article  Google Scholar 

  39. Simões D, de CM, McNeill D, Kristiansen B, Mattey M (1997) Purification and partial characterisation of a 1.57 kDa thermostable esterase from Bacillus stearothermophilus. FEMS Microbiol Lett 147:151–156. https://doi.org/10.1111/j.1574-6968.1997.tb10235.x

    Article  Google Scholar 

  40. Fan X, Mattey M (1999) Small enzymes with esterase activities from two thermophilic fungi, Emericella nidulans and Talaromyces Emersonii. Biotechnol Lett 21:1071–1076. https://doi.org/10.1023/A:1005601030076

    Article  CAS  Google Scholar 

  41. Hu J, Li D, Su X-D et al (2010) Solution structure and conformational heterogeneity of acylphosphatase from Bacillus subtilis. FEBS Lett 584:2852–2856. https://doi.org/10.1016/j.febslet.2010.04.069

    Article  CAS  PubMed  Google Scholar 

  42. Bhardwaj K, Raju A, Rajasekharan R (2001) Identification, purification, and characterization of a thermally stable lipase from Rice Bran. A New Member of the (Phospho) Lipase Family. Plant Physiol 127:1728–1738

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Kanauchi M, Simon KJ, Bamforth CW (2014) Ascorbic acid oxidase in Barley and Malt and its possible role during Mashing. J Am Soc Brew Chem 72:30–35. https://doi.org/10.1094/ASBCJ-2014-0120-01

    Article  CAS  Google Scholar 

  44. Rabert C, Gutiérrez-Moraga A, Navarrete-Gallegos A et al (2014) Expression of a Deschampsia antarctica Desv. Polypeptide with lipase activity in a Pichia pastoris Vector. Int J Mol Sci 15:2359–2367. https://doi.org/10.3390/ijms15022359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Papagianni M, Papamichael EM (2017) Purification, amino acid sequencing and thermostability of an extracellular low molecular weight esterase produced by Bacillus subtilis NRRL 41270 in fermentation. J Microb Biochem Technol 9:117–121. https://doi.org/10.4172/1948-5948.1000353

    Article  CAS  Google Scholar 

  46. Arpigny JL, Jaeger KE (1999) Bacterial lipolytic enzymes: classification and properties. Biochem J 343 Pt 1:177–183

    Article  Google Scholar 

  47. Maldonado MR, Alnoch RC, de Almeida JM, et al (2021) Key mutation sites for improvement of the enantioselectivity of lipases through protein engineering. Biochem Eng J 172:108047. https://doi.org/10.1016/j.bej.2021.108047

  48. Akoh CC, Lee G-C, Liaw Y-C et al (2004) GDSL family of serine esterases/lipases. Prog Lipid Res 43:534–552. https://doi.org/10.1016/j.plipres.2004.09.002

    Article  CAS  PubMed  Google Scholar 

  49. Yamashiro T, Shiraishi A, Nakayama K, Satake H (2022) Key amino acids for transferase activity of GDSL lipases. Int J Mol Sci 23:15141. https://doi.org/10.3390/ijms232315141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Wang J, Zhao H, Qu Y et al (2022) The binding pocket properties were fundamental to functional diversification of the GDSL-type esterases/lipases gene family in cotton. Front Plant Sci 13:1099673. https://doi.org/10.3389/fpls.2022.1099673

    Article  PubMed  Google Scholar 

  51. Castleden I Wheat Proteome. In: Wheat Proteome. https://wheatproteome.org. Accessed 2 Dec 2023

  52. Leščić Ašler I, Štefanić Z, Maršavelski A et al (2017) Catalytic Dyad in the SGNH Hydrolase Superfamily: In-depth insight into structural parameters tuning the Catalytic process of Extracellular lipase from Streptomyces rimosus. ACS Chem Biol 12:1928–1936. https://doi.org/10.1021/acschembio.6b01140

    Article  CAS  PubMed  Google Scholar 

  53. Jumper J, Evans R, Pritzel A et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583–589. https://doi.org/10.1038/s41586-021-03819-2

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  54. Pettersen EF, Goddard TD, Huang CC et al (2021) UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci 30:70–82. https://doi.org/10.1002/pro.3943

    Article  CAS  PubMed  Google Scholar 

  55. Stefani M, Taddei N, Ramponi G (1997) Insights into acylphosphatase structure and catalytic mechanism. CMLS Cell Mol life sci 53:141–151. https://doi.org/10.1007/PL00000585

    Article  CAS  PubMed  Google Scholar 

  56. Corazza A, Rosano C, Pagano K et al (2006) Structure, conformational stability, and enzymatic properties of acylphosphatase from the hyperthermophile Sulfolobus solfataricus. Proteins Struct Funct Bioinform 62:64–79. https://doi.org/10.1002/prot.20703

    Article  CAS  Google Scholar 

  57. Degl’Innocenti D, Ramazzotti M, Marzocchini R et al (2003) Characterization of a novel Drosophila melanogaster acylphosphatase. FEBS Lett 535:171–174. https://doi.org/10.1016/S0014-5793(02)03901-7

    Article  PubMed  Google Scholar 

  58. Miyazono K, Sawano Y, Tanokura M (2004) Crystal structure of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3. Proc Jpn Acad Ser B Phys Biol Sci 80:439–442

    Article  ADS  CAS  PubMed Central  Google Scholar 

  59. Thunnissen MM, Taddei N, Liguri G et al (1997) Crystal structure of common type acylphosphatase from bovine testis. Structure 5:69–79. https://doi.org/10.1016/S0969-2126(97)00167-6

    Article  CAS  PubMed  Google Scholar 

  60. Zouari Ayadi D, Ben Ali M, Jemli S et al (2008) Heterologous expression, secretion and characterization of the Geobacillus thermoleovorans US105 type I pullulanase. Appl Microbiol Biotechnol 78:473–481. https://doi.org/10.1007/s00253-007-1318-9

    Article  CAS  PubMed  Google Scholar 

  61. Chen A, Sun Y, Zhang W et al (2016) Downsizing a pullulanase to a small molecule with improved soluble expression and secretion efficiency in Escherichia coli. Microb Cell Fact 15:9. https://doi.org/10.1186/s12934-015-0403-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Ameyama M, Shinagawa E, Matsushita K, Adachi O (1981) D-fructose dehydrogenase of Gluconobacter industrius: purification, characterization, and application to enzymatic microdetermination of D-fructose. J Bacteriol 145:814–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Kawai S, Goda-Tsutsumi M, Yakushi T et al (2013) Heterologous overexpression and characterization of a flavoprotein-cytochrome c complex fructose dehydrogenase of Gluconobacter japonicus NBRC3260. Appl Environ Microbiol 79:1654–1660. https://doi.org/10.1128/AEM.03152-12

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  64. Kaida Y, Hibino Y, Kitazumi Y et al (2019) Ultimate downsizing of d-fructose dehydrogenase for improving the performance of direct electron transfer-type bioelectrocatalysis. Electrochem Commun 98:101–105. https://doi.org/10.1016/j.elecom.2018.12.001

    Article  CAS  Google Scholar 

  65. Kitts DD, Weiler K (2003) Bioactive proteins and peptides from food sources. Applications of bioprocesses used in isolation and recovery. Curr Pharm Des 9:1309–1323. https://doi.org/10.2174/1381612033454883

    Article  CAS  PubMed  Google Scholar 

  66. Sánchez A, Vázquez A (2017) Bioactive peptides: a review. Food Qual Saf 1:29–46. https://doi.org/10.1093/fqsafe/fyx006

    Article  CAS  Google Scholar 

  67. Akbarian M, Khani A, Eghbalpour S, Uversky VN (2022) Bioactive peptides: synthesis, sources, applications, and proposed mechanisms of action. Int J Mol Sci 23:1445. https://doi.org/10.3390/ijms23031445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Sousa ME, Farkas MH (2018) Micropeptide. PLoS Genet 14:e1007764. https://doi.org/10.1371/journal.pgen.1007764

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Tacias-Pascacio VG, Castañeda-Valbuena D, Tavano O et al (2023) Peptides with biological and technofunctional properties produced by bromelain hydrolysis of proteins from different sources: a review. Int J Biol Macromol 253:127244. https://doi.org/10.1016/j.ijbiomac.2023.127244

    Article  CAS  PubMed  Google Scholar 

  70. Tanaka H, Itakura S, Hirano T, Enoki A (1996) An extracellular substance from the white-rot basidiomycete Phanerochaete chrysosporium for reducing molecular oxygen and ferric iron. Holzforschung 50:541–548. https://doi.org/10.1515/hfsg.1996.50.6.541

    Article  CAS  Google Scholar 

  71. Tanaka H, Itakura S, Enoki A (1999) Hydroxyl radical generation by an extracellular low-molecular-weight substance and phenol oxidase activity during wood degradation by the white-rot basidiomycete Trametes Versicolor. J Biotechnol 75:57–70. https://doi.org/10.1016/s0168-1656(99)00138-8

    Article  CAS  PubMed  Google Scholar 

  72. Tanaka H, Yoshida G, Baba Y et al (2007) Characterization of a hydroxyl-radical-producing glycoprotein and its presumptive genes from the white-rot basidiomycete Phanerochaete Chrysosporium. J Biotechnol 128:500–511. https://doi.org/10.1016/j.jbiotec.2006.12.010

    Article  CAS  PubMed  Google Scholar 

  73. Arantes V, Milagres AMF (2009) Relevância de compostos de baixa massa molar produzidos por fungos e envolvidos na biodegradação da madeira. Quím Nova 32:1586–1595. https://doi.org/10.1590/S0100-40422009000600043

    Article  CAS  Google Scholar 

  74. Freitas EN, Salgado JC, Alnoch RC et al (2021) Challenges of biomass utilization for bioenergy in a climate change scenario. Biology 10:1277. https://doi.org/10.3390/biology10121277

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Harris D, DeBolt S (2010) Synthesis, regulation and utilization of lignocellulosic biomass. Plant Biotechnol J 8:244–262. https://doi.org/10.1111/j.1467-7652.2009.00481.x

    Article  CAS  PubMed  Google Scholar 

  76. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66:506–577. https://doi.org/10.1128/MMBR.66.3.506-577.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Bhatia Y, Mishra S, Bisaria VS (2002) Microbial beta-glucosidases: cloning, properties, and applications. Crit Rev Biotechnol 22:375–407. https://doi.org/10.1080/07388550290789568

    Article  CAS  PubMed  Google Scholar 

  78. Polizeli MLTM, Rizzatti ACS, Monti R et al (2005) Xylanases from fungi: properties and industrial applications. Appl Microbiol Biotechnol 67:577–591. https://doi.org/10.1007/s00253-005-1904-7

    Article  CAS  PubMed  Google Scholar 

  79. Qing Q, Yang B, Wyman CE (2010) Xylooligomers are strong inhibitors of cellulose hydrolysis by enzymes. Bioresour Technol 101:9624–9630. https://doi.org/10.1016/j.biortech.2010.06.137

    Article  CAS  PubMed  Google Scholar 

  80. Buckeridge MS, Santos WD, Tiné MAS, Souza AP (2015) The Cell Wall Architecture of Sugarcane and its Implications to Cell Wall Recalcitrance. In: Compendium of Bioenergy Plants. CRC Press, p 31–50

  81. Maziero P, Jong J, Mendes FM et al (2013) Tissue-specific cell wall hydration in sugarcane stalks. J Agric Food Chem 61:5841–5847. https://doi.org/10.1021/jf401243c

    Article  CAS  PubMed  Google Scholar 

  82. Baron-Epel O, Hernandez D, Jiang LW et al (1988) Dynamic continuity of cytoplasmic and membrane compartments between plant cells. J Cell Biol 106:715–721. https://doi.org/10.1083/jcb.106.3.715

    Article  CAS  PubMed  Google Scholar 

  83. Carpita NC (1982) Limiting diameters of pores and the surface structure of plant cell walls. Science 218:813–814. https://doi.org/10.1126/science.218.4574.813

    Article  ADS  CAS  PubMed  Google Scholar 

  84. Buckeridge MS, De Souza AP, Arundale RA et al (2012) Ethanol from sugarcane in Brazil: a ‘midway’ strategy for increasing ethanol production while maximizing environmental benefits. GCB Bioenergy 4:119–126. https://doi.org/10.1111/j.1757-1707.2011.01122.x

    Article  CAS  Google Scholar 

  85. Evans JR, Caemmerer SV, Setchell BA, Hudson GS (1994) The relationship between CO2 transfer conductance and leaf anatomy in transgenic tobacco with a reduced content of Rubisco. Funct Plant Biol 21:475–495. https://doi.org/10.1071/pp9940475

    Article  CAS  Google Scholar 

  86. Yang W, Liu J, Wang W et al (2004) Function of a low molecular peptide generated by cellulolytic fungi for the degradation of native cellulose. Biotechnol Lett 26:1799–1802. https://doi.org/10.1007/s10529-004-4612-y

    Article  CAS  PubMed  Google Scholar 

  87. Comings DE (1972) The structure and function of chromatin. Adv Hum Genet 3:237–431. https://doi.org/10.1007/978-1-4757-4429-3_5

    Article  CAS  PubMed  Google Scholar 

  88. Ohno S (1972) So much junk DNA in our genome. Brookhaven Symp Biol 23:366–370

    CAS  PubMed  Google Scholar 

  89. Papadopoulos C (2022) The noncoding genome, a reservoir of genetic novelty. Quantitative Methods [q-bio.QM]. PhD Thesis, Université Paris-Saclay

  90. Yin X, Jing Y, Xu H (2019) Mining for missed sORF-encoded peptides. Expert Rev Proteom 16:257–266. https://doi.org/10.1080/14789450.2019.1571919

    Article  CAS  Google Scholar 

  91. Ma J, Ward CC, Jungreis I et al (2014) Discovery of human sORF-Encoded polypeptides (SEPs) in cell lines and tissue. J Proteome Res 13:1757–1765. https://doi.org/10.1021/pr401280w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. de Crécy-lagard V, Amorin de Hegedus R, Arighi C et al (2022) A roadmap for the functional annotation of protein families: a community perspective. Database (Oxford) 2022:baac062. https://doi.org/10.1093/database/baac062

    Article  CAS  PubMed  Google Scholar 

  93. Pandey AK, Lu L, Wang X et al (2014) Functionally enigmatic genes: a case study of the brain ignorome. PLoS ONE 9:e88889. https://doi.org/10.1371/journal.pone.0088889

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  94. Siddiq MA, Hochberg GK, Thornton JW (2017) Evolution of protein specificity: insights from ancestral protein reconstruction. Curr Opin Struct Biol 47:113–122. https://doi.org/10.1016/j.sbi.2017.07.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. de Crécy-Lagard V (2014) Variations in metabolic pathways create challenges for automated metabolic reconstructions: examples from the tetrahydrofolate synthesis pathway. Comput Struct Biotechnol J 10:41–50. https://doi.org/10.1016/j.csbj.2014.05.008

    Article  PubMed  PubMed Central  Google Scholar 

  96. Fiser A, Šali A (2003) Modeller: generation and refinement of homology-based protein structure models. In: Methods in enzymology. Academic, pp 461–491

  97. Biasini M, Bienert S, Waterhouse A et al (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42:W252–W258. https://doi.org/10.1093/nar/gku340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Schymkowitz J, Borg J, Stricher F et al (2005) The FoldX web server: an online force field. Nucleic Acids Res 33:W382–W388. https://doi.org/10.1093/nar/gki387

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Peng J, Xu J (2011) Raptorx: exploiting structure information for protein alignment by statistical inference. Proteins Struct Funct Bioinform 79:161–171. https://doi.org/10.1002/prot.23175

    Article  Google Scholar 

  100. Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244–W248. https://doi.org/10.1093/nar/gki408

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Ghouzam Y, Postic G, Guerin P-E et al (2016) ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. Sci Rep 6:28268. https://doi.org/10.1038/srep28268

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  102. Kuhlman B, Bradley P (2019) Advances in protein structure prediction and design. Nat Rev Mol Cell Biol 20:681–697. https://doi.org/10.1038/s41580-019-0163-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Perrakis A, Sixma TK (2021) AI revolutions in biology: the joys and perils of AlphaFold. EMBO Rep 22:e54046. https://doi.org/10.15252/embr.202154046

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

The authors gratefully acknowledge Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP – 2023/01547-5), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq − 310840/2021-0; 310340/2021-7) and the Instituto Nacional de Ciência e Tecnologia do Bioetanol (INCT - CNPq 465319/2014-9/FAPESP n° 2014/50884-5) for financial support. Research scholarships were granted by FAPESP to JCSS (n° 2019/21989-7) and RCA (n° 2020/00081−4), by CNPq to JCSS (384465/2023-4), and by CNPq/FAPESP to RCA ( CNPq 151187/2023-1/FAPESP n° 2023/09627-8).

Author information

Authors and Affiliations

Authors

Contributions

J.C.S.S. and R.J.W. conceived the study; J.C.S.S. and R.C.A. performed the literature search and wrote the original draft; M.L.T.M.P. and R.J.W. critically revised the work. All authors reviewed and approved the final manuscript.

Corresponding author

Correspondence to Jose Carlos Santos Salgado.

Ethics declarations

Ethical Approval

Not Applicable.

Consent to Participate

Not applicable.

Consent for Publication

Not applicable.

Competing Interests

The authors declare no competing interests.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Salgado, J.C.S., Alnoch, R.C., Polizeli, M.d.L.T.d.M. et al. Microenzymes: Is There Anybody Out There?. Protein J (2024). https://doi.org/10.1007/s10930-024-10193-1

Download citation

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10930-024-10193-1

Keywords

Navigation