• Saeid KadkhodaeiEmail author
  • Farahnaz Sadat Golestan Hashemi
  • Morvarid Akhavan Rezaei
  • Sahar Abbasiliasi
  • Joo Shun Tan
  • Hamid Rajabi Memari
  • Faruku Bande
  • Ali Baradaran
  • Mahdi Moradpour
  • Arbakariya B. Ariff
Part of the SpringerBriefs in Systems Biology book series (BRIEFSBIOSYS)


In recombinant protein production, quantity and quality are the major challenges, particularly in scale-up and high-throughput production systems. The present practical review uses computational analysis and in silico approaches for the systematic discovery of novel functional gene expression elements in microalgae, which has not been thoroughly studied. This introduction outlines the matrix attachment regions (MARs), translation initiation sites (TIS), signal peptide (SP) sequences, gene optimization, and transformation systems.


Computational biology Gene optimization Matrix attachment regions Signal peptide Translation initiation sites 


  1. 1.
    Agalarov SC, Sogorin EA, Shirokikh NE, Spirin AS (2011) Insight into the structural organization of the omega leader of TMV RNA: the role of various regions of the sequence in the formation of a compact structure of the omega RNA. Biochem Biophys Res Commun 404:250–253. Scholar
  2. 2.
    Arope S, Harraghy N, Pjanic M, Mermod N (2013) Molecular characterization of a human matrix attachment region epigenetic regulator. PLoS ONE 8:e79262. Scholar
  3. 3.
    Barnes D, Franklin S, Schultz J, Henry R, Brown E, Coragliotti A, Mayfield SP (2005) Contribution of 5′- and 3′-untranslated regions of plastid mRNAs to the expression of Chlamydomonas reinhardtii chloroplast genes. Mol Genet Genomics 274:625–636. Scholar
  4. 4.
    Bellucci M, Alpini A, Paolocci F, Cong L, Arcioni S (2000) Accumulation of maize γ-zein and γ-zein: KDEL to high levels in tobacco leaves and differential increase of BiP synthesis in transformants. TAG Theor Appl Genet 101:796–804. Scholar
  5. 5.
    Capitani M, Sallese M (2009) The KDEL receptor: new functions for an old protein. FEBS Lett 583:3863–3871. Scholar
  6. 6.
    Cavener DR (1987) Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates. Nucleic Acids Res 15:1353–1361. Scholar
  7. 7.
    Cavener DR, Ray SC (1991) Eukaryotic start and stop translation sites. Nucleic Acids Res 19:3185–3192. Scholar
  8. 8.
    Coragliotti AT, Beligni MV, Franklin SE, Mayfield SP (2011) Molecular factors affecting the accumulation of recombinant proteins in the Chlamydomonas reinhardtii chloroplast. Mol Biotechnol 48:60–75. Scholar
  9. 9.
    Doran PM (2006) Foreign protein degradation and instability in plants and plant tissue cultures. Trends Biotechnol 24:426–432. Scholar
  10. 10.
    Fukuda S, Mikami K, Uji T, Park E-J, Ohba T, Asada K, Kitade Y, Endo H, Kato I, Saga N (2008) Factors influencing efficiency of transient gene expression in the red macrophyte Porphyra yezoensis. Plant Sci 174:329–339. Scholar
  11. 11.
    Geli MI, Torrent M, Ludevid D (1994) Two structural domains mediate two sequential events in [gamma]-zein targeting: protein endoplasmic reticulum retention and protein body formation. Plant Cell 6:1911–1922. Scholar
  12. 12.
    Geng L, Chi J, Shu C, Gresshoff PM, Song F, Huang D, Zhang J (2013) A chimeric cry8Ea1 gene flanked by MARs efficiently controls Holotrichia parallela. Plant Cell Rep 32:1211–1218. Scholar
  13. 13.
    Gomord V, Denmat L-A, Fitchette-Laine A-C, Satiat-Jeunemaitre B, Hawes C, Faye L (1997) The C-terminal HDEL sequence is sufficient for retention of secretory proteins in the endoplasmic reticulum (ER) but promotes vacuolar targeting of proteins that escape the ER. Plant J 11:313–325. Scholar
  14. 14.
    Gorman C, Arope S, Grandjean M, Girod P, Mermod N (2009) Use of MAR elements to increase the production of recombinant proteins. In: Al-Rubeai M (ed) Cell line development, cell engineering 6. Springer, Netherlands, Dordrecht, pp 1–32Google Scholar
  15. 15.
    Grandjean M, Girod P-A, Calabrese D, Kostyrko K, Wicht M, Yerly F, Mazza C, Beckmann JS, Martinet D, Mermod N (2011) High-level transgene expression by homologous recombination-mediated gene transfer. Nucleic Acids Res 39:1–15. Scholar
  16. 16.
    Gustafsson C, Govindarajan S, Minshull J (2004) Codon bias and heterologous protein expression. Trends Biotechnol 22:346–353. Scholar
  17. 17.
    Hamilton R, Watanabe CK, Deboer HA (1987) Compliation and comparison of the sequence context around the AUG startcodons in Saccharomyces cerevisiae messenger-RNAs. Nucleic Acids Res 15:3581–3593. Scholar
  18. 18.
    Joshi CP, Zhou H, Huang X, Chiang VL (1997) Context sequences of translation initiation codon in plants. Plant Mol Biol 35:993–1001. Scholar
  19. 19.
    Kozak M (1987) At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells. J Mol Biol 196:947–950. Scholar
  20. 20.
    Kozak M (1987) An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res 15:8125–8148. Scholar
  21. 21.
    Lorimer D, Raymond A, Walchli J, Mixon M, Barrow A, Wallace E, Grice R, Burgin A, Stewart L (2009) Gene composer: database software for protein construct design, codon engineering, and gene synthesis. BMC Biotechnol 9:36. Scholar
  22. 22.
    Lütcke HA, Chow KC, Mickel FS, Moss KA, Kern HF, Scheele GA (1987) Selection of AUG initiation codons differs in plants and animals. EMBO J 6:43–48PubMedPubMedCentralCrossRefGoogle Scholar
  23. 23.
    Matsukawa S, Moriyama Y, Hayata T, Sasaki H, Ito Y, Asashima M, Kuroda H (2012) KDEL tagging: a method for generating dominant-negative inhibitors of the secretion of TGF-beta superfamily proteins. Int J Dev Biol 56:351–356. Scholar
  24. 24.
    Merrick WC, Hershey JW (1996) The pathway and mechanism of Eukaryotic protein synthesis. In: Translational control of gene expression. Cold Spring Harbor Laboratory Press, New York, pp 31–69Google Scholar
  25. 25.
    Mundembe R (2013) Gene targeting and genetic transformation of plants. In: Genetic engineering. InTech, LondonGoogle Scholar
  26. 26.
    Muto M, Henry RE, Mayfield SP (2009) Accumulation and processing of a recombinant protein designed as a cleavable fusion to the endogenous Rubisco LSU protein in Chlamydomonas chloroplast. BMC Biotechnol 9:26. Scholar
  27. 27.
    De Muynck B, Navarre C, Boutry M (2010) Production of antibodies in plants: status after twenty years. Plant Biotechnol J 8:529–563. Scholar
  28. 28.
    Nakamura Y, Gojobori T, Ikemura T (1999) Codon usage tabulated from the international DNA sequence databases; its status 1999. Nucleic Acids Res 27:292. Scholar
  29. 29.
    Nowak W, Gawłowska M, Jarmołowski A, Augustyniak J (2001) Effect of nuclear matrix attachment regions on transgene expression in tobacco plants. Acta Biochim Pol 48:637–646PubMedGoogle Scholar
  30. 30.
    Obembe OO, Popoola JO, Leelavathi S, Reddy SV (2011) Advances in plant molecular farming. Biotechnol Adv 29:210–222. Scholar
  31. 31.
    Padmaja SS, Lakshmanan J, Gupta R, Banerjee S, Gautam P, Banerjee S (2010) Identification of Scaffold/matrix attachment (S/MAR) like DNA element from the gastrointestinal protozoan parasite Giardia lamblia. BMC Genom 11:386. Scholar
  32. 32.
    Rademacher T, Sack M, Arcalis E, Stadlmann J, Balzer S, Altmann F, Quendler H, Stiegler G, Kunert R, Fischer R, Stoger E (2008) Recombinant antibody 2G12 produced in maize endosperm efficiently neutralizes HIV-1 and contains predominantly single-GlcNAc N-glycans. Plant Biotechnol J 6:189–201. Scholar
  33. 33.
    Rogozin IB (2000) Computer prediction of sites associated with various elements of the nuclear matrix. Brief Bioinform 1:33–44. Scholar
  34. 34.
    Rybicki EP (2010) Plant-made vaccines for humans and animals. Plant Biotechnol J 8:620–637. Scholar
  35. 35.
    Schillberg S, Zimmermann S, Voss A, Fischer R (1999) Apoplastic and cytosolic expression of full-size antibodies and antibody fragments in Nicotiana tabacum. Transgenic Res 8:255–263. Scholar
  36. 36.
    Seeber F (1997) Consensus sequence of translational initiation sites from Toxoplasma gondii genes. Parasitol Res 83:309–311. Scholar
  37. 37.
    Shaaltiel Y, Bartfeld D, Hashmueli S, Baum G, Brill-Almon E, Galili G, Dym O, Boldin-Adamsky SA, Silman I, Sussman JL, Futerman AH, Aviezer D (2007) Production of glucocerebrosidase with terminal mannose glycans for enzyme replacement therapy of Gaucher’s disease using a plant cell system. Plant Biotechnol J 5:579–590. Scholar
  38. 38.
    Sørensen HP, Mortensen KK (2005) Advanced genetic strategies for recombinant protein expression in Escherichia coli. J Biotechnol 115:113–128. Scholar
  39. 39.
    Stoger E, Ma JK-C, Fischer R, Christou P (2005) Sowing the seeds of success: pharmaceutical proteins from plants. Curr Opin Biotechnol 16:167–173. Scholar
  40. 40.
    Streatfield SJ (2007) Approaches to achieve high-level heterologous protein production in plants. Plant Biotechnol J 5:2–15. Scholar
  41. 41.
    Tetko IV, Haberer G, Rudd S, Meyers B, Mewes H, Mayer KFX (2006) Spatiotemporal expression control correlates with intragenic Scaffold Matrix Attachment regions (S/MARs) in Arabidopsis thaliana. PLoS Comput Biol 2:e21. Scholar
  42. 42.
    Vimberg V, Tats A, Remm M, Tenson T (2007) Translation initiation region sequence preferences in Escherichia coli. BMC Mol Biol 8:100. Scholar
  43. 43.
    Wang A, Ma S (2012) Molecular farming in plants: recent advances and future prospects. Springer, Netherlands, DordrechtCrossRefGoogle Scholar
  44. 44.
    Wang F, Wang T-Y, Tang Y-Y, Zhang J-H, Yang X-J (2012) Different matrix attachment regions flanking a transgene effectively enhance gene expression in stably transfected Chinese hamster ovary cells. Gene 500:59–62. Scholar
  45. 45.
    Wang T, Xue L, Hou W, Yang B, Chai Y, Ji X, Wang Y (2007) Increased expression of transgene in stably transformed cells of Dunaliella salina by matrix attachment regions. Appl Microbiol Biotechnol 76:651–657. Scholar
  46. 46.
    Yamauchi K (1991) The sequence flanking translational initiation site in protozoa. Nucleic Acids Res 19:2715–2720. Scholar

Copyright information

© The Author(s) 2018

Authors and Affiliations

  • Saeid Kadkhodaei
    • 1
    Email author
  • Farahnaz Sadat Golestan Hashemi
    • 2
  • Morvarid Akhavan Rezaei
    • 3
  • Sahar Abbasiliasi
    • 4
  • Joo Shun Tan
    • 5
  • Hamid Rajabi Memari
    • 6
  • Faruku Bande
    • 7
  • Ali Baradaran
    • 8
    • 9
  • Mahdi Moradpour
    • 10
  • Arbakariya B. Ariff
    • 11
  1. 1.Research Institute for Biotechnology and BioengineeringIsfahan University of TechnologyIsfahanIran
  2. 2.Plant Genetics, AgroBioChem Department, Gembloux Agro-Bio TechUniversity of LiègeLiègeBelgium
  3. 3.Tropical Infectious Diseases Research and Education Centre (TIDREC), Faculty of MedicineUniversity of MalayaKuala LumpurMalaysia
  4. 4.Halal Products Research InstituteUniversiti Putra MalaysiaSeri KembanganMalaysia
  5. 5.Bioprocess Technology, School of Industrial TechnologyUniversiti Sains MalaysiaGeorge Town, PenangMalaysia
  6. 6.SynHiTechThornhillCanada
  7. 7.Department of Veterinary Services, Ministry of Animal Health and Fisheries DevelopmentUsman Faruk Secretariat, SokotoSokotoNigeria
  8. 8.Mater ResearchTranslational Research InstituteWoolloongabbaAustralia
  9. 9.Faculty of Medicine, Translational Research Institute, Diamantina InstituteUniversity of QueenslandBrisbaneAustralia
  10. 10.Institute of plantation studiesUniversiti Putra MalaysiaSeri KembanganMalaysia
  11. 11.Faculty of Biotechnology and Biomolecular SciencesUniversiti Putra MalaysiaSeri KembanganMalaysia

Personalised recommendations