Sequence Analysis of the Cas1 Gene in Riemerella anatipestifer

Abstract:

Objective: The aim was to analyze Riemerella anatipestifer (RA) Cas1 gene and acquire more useful information for guiding the further study of the gene. Methods: Using bioinformatics method, sequence analysis of RA Cas1 gene was carried out with some databases and software. Results: Composition analysis of RA Cas1 gene, and homology search, sequence alignment, phylogenetic tree analysis and physicochemical property analysis of RA Cas1 protein were performed. Homology search revealed that Cas1 protein sequence of R. anatipestifer showed high similarity to those of strains within the Genus Capnocytophaga and Chryseobacterium, in accordance with the result of multiple sequence alignment and phylogenetic tree analysis. The rare codon analysis showed that there was little rare codon string in RA Cas1 gene. Conclusion: Cas1 gene of R. anatipestifer was evolutionally closely related to those of the Genus Capnocytophaga and Chryseobacterium, and can be over-expressed in E.coli without considering the impact of rare codons on translation.

• Periodical: Advanced Materials Research (Volumes 641-642)
• Pages: 797-802
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.641-642.797
• Online since: January 2013
• Authors: Yang He, An Chun Cheng, Ming Shu Wang, De Kang Zhu, Xiao Jia Wang, Xin Zhang
• Keywords: Bioinformatics, Cas1 Gene, CRISPR-Cas System, Riemerella anatipestifer, Sequence Analysis

References

[1] Y. M. Saif, A. M. Fadly, and J. R. Glisson, Diseases of Poultry, twelfth ed., Blackwell Pub., 2008.

[2] P. Pathanasophon, T. Sawada, and T. Tanticharoenyos, New serotypes of Riemerella anatipestifer isolated from ducks in Thailand, Avian Pathol, 24 (Mar 1995) 195-199.

DOI: 10.1080/03079459508419059

[3] P. Pathanasophon, P. Phuektes, T. Tanticharoenyos, W. Narongsak, and T. Sawada, A potential new serotype of Riemerella anatipestifer isolated from ducks in Thailand, Avian Pathol, 31 (Jun 2002) 267-270.

DOI: 10.1080/03079450220136576

[4] C. AnChun, W. MingShu, C. XiaoYue, Z. DeKang, H. Cheng, L. Fei, Z. Yi, G. YuFei, L. ZhaoYu, and F. PengFei, Epidemiology and New Serotypes of Riemerella anatipestifer Isolated from Ducks in China and Studies on Their Pathogenic Characteristics, Chin. J. Vet. Sci., 23 (2003) 320-323.

[5] K. Brogden, K. Rhoades, and R. Rimler, Serologic types and physiologic characteristics of 46 avian Pasteurella anatipestifer cultures, Avian Diseases, (1982) 891-896.

DOI: 10.2307/1589877

[6] T. Sandhu, M. L. Leister, Serotypes of 'Pasteurella' anatipestifer isolates from poultry in different countries, Avian Pathology, 20 (1991) 233-239.

DOI: 10.1080/03079459108418760

[7] M. Ryl, K. Hinz, Exclusion of strain 670/89 as type strain for serovar 20 of Riemerella anatipestifer, Berliner und Münchener tierärztliche Wochenschrift, 113 (2000) 65.

[8] W. Xiaojia, Z. DeKang, W. MingShu, C. AnChun, J. RenYong, Z. Yi, C. Zhengli, L. QiHui, L. Fei, W. Yi, and C. XiaoYue, Complete Genome Sequence of Riemerella anatipestifer Reference Strain, Journal of Bacteriology, 194 (2012) 3270-3271.

DOI: 10.1637/9333-917210-digest.1

[9] D. H. Haft, J. Selengut, E. F. Mongodin, and K. E. Nelson, A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes, PLoS computational biology, 1 (2005) 60.

DOI: 10.1371/journal.pcbi.0010060

[10] S. J. J. Brouns, M. M. Jore, M. Lundgren, E. R. Westra, R. J. H. Slijkhuis, A. P. L. Snijders, M. J. Dickman, K. S. Makarova, E. V. Koonin, and J. Van der Oost, Small CRISPR RNAs guide antiviral defense in prokaryotes, Science, 321 (2008) 960-964.

DOI: 10.1126/science.1159689

[11] K. S. Makarova, L. Aravind, Y. I. Wolf, and E. V. Koonin, Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems, Biology Direct, 6 (2011)38.

DOI: 10.1186/1745-6150-6-38

[12] K. S. Makarova, N. V. Grishin, S. A. Shabalina, Y. I. Wolf, and E. V. Koonin, A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action, Biology Direct, 1 (2006) 7.

DOI: 10.1186/1745-6150-1-7

[13] H. Deveau, J. E. Garneau, and S. Moineau, CRISPR/Cas system and its role in phage-bacteria interactions, Annual review of microbiology, 64 (2010) 475-493.

DOI: 10.1146/annurev.micro.112408.134123

[14] H. Yang, C. Anchun, and W. Mingshu, Analysis of Synonymous Codon Usage in the Cas1 Gene of Riemerella anatipestifer, Accepted for presentation at 5th International Conference on BioMedical Engineering and Informatics (BMEI'12), (2012).

DOI: 10.1109/bmei.2012.6512980

[15] R. B. Russell, Genomics, proteomics and bioinformatics: all in the same boat, Genome Biology, 3 (2002) 4034.

[16] S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic acids research, 25 (1997) 3389-3402.

DOI: 10.1093/nar/25.17.3389

[17] J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Research, 25 (Dec 15 1997) 4876-4882.

DOI: 10.1093/nar/25.24.4876

[18] K. Tamura, J. Dudley, M. Nei, and S. Kumar, MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0, Molecular Biology and Evolution, 24 (2007) 1596-1599.

DOI: 10.1093/molbev/msm092

[19] P. Schenk, S. Baumann, R. Mattes, and H. H. Steinbiss, Improved high-level expression system for eukaryotic genes in Escherichia coli using T7 RNA polymerase and rare ArgtRNAs, BioTechniques, 19 (1995) 196-200.

[20] T. K. Attwood, The role of pattern databases in sequence analysis, Briefings in bioinformatics, 1 (2000) 45-59.

DOI: 10.1093/bib/1.1.45

[21] C. P. Carstens, A. Waesche, Codon bias-adjusted BL21 derivatives for protein expression, Strategies Newsletters (Stratagene), 12 (1999) 49-51.