EC Microbiology

Research Article Volume 19 Issue 3 - 2023

Peptide Properties of Saccharomyces arboricola H-6 Suggest Randomness in Chromosomal Organization

Daeun Roh1,2, Shah Yunn Naing1,2 and Maurice HT Ling1,2,3*

1School of Life Sciences, Management Development Institute of Singapore, Singapore

2School of Applied Sciences, Northumbria University, United Kingdom

3HOHY PTE LTD, Singapore

*Corresponding Author: Maurice HT Ling, School of Life Sciences, Management Development Institute of Singapore and School of Applied Sciences, Northumbria University, United Kingdom and HOHY PTE LTD, Singapore.
Received: February 02, 2023; Published: February 28, 2023

Eukaryotic genomes are organized into multiple chromosomes and studies have suggested that chromosomal organization is subjected to evolutionary pressure as demonstrated by non-randomness of properties across chromosomes. However, a recent study provided evidence to suggest that chromosomal organization may be more random in unicellular than multicellular eukaryotes. Here, we examine the distribution of five peptide features (length, aromaticity, instability, hydropathy, and isoelectric point) across the 16 nuclear chromosomes of Saccharomyces arboricola H-6, a recently identified and sequenced unicellular eukaryote. Our results show that only hydropathy is not random across the chromosomes (F = 1.914, p-value = 0.018); thereby, supporting the hypothesis that chromosomal organization may be random in unicellular eukaryotes.

Keywords: Peptide Properties; Saccharomyces arboricola H-6; Chromosomal Organization

  1. Wang S-A and Bai F-Y. “Saccharomyces arboricolus nov., A Yeast Species from Tree Bark”. International Journal of Systematic and Evolutionary Microbiology 58.2 (2008): 510-514.
  2. Gayevskiy V and Goddard MR. “Saccharomyces eubayanus and Saccharomyces arboricola Reside in North Island Native New Zealand Forests”. Environmental Microbiology4 (2016): 1137-1147.
  3. Naumov GI. “Hybridization Analysis of the New Biological Species Saccharomyces arboricolus Wang et Bai”. Doklady Biological Sciences: Proceedings of the Academy of Sciences of the USSR, Biological Sciences Sections 426 (2009): 247-249.
  4. Naumov GI., et al. “Genetic Identification of New Biological Species Saccharomyces arboricolus Wang et Bai”. Antonie Van Leeuwenhoek1 (2010): 1-7.
  5. Muir A., et al. “A Multiplex Set of Species-Specific Primers for Rapid Identification of Members of the Genus Saccharomyces”. FEMS Yeast Research7 (2011): 552-563.
  6. Naumov GI., et al. “Molecular Genetic Diversity of the Saccharomyces Yeasts in Taiwan: Saccharomyces arboricola, Saccharomyces cerevisiae and Saccharomyces kudriavzevii”. Antonie Van Leeuwenhoek1 (2013): 217-228.
  7. Magalhães F., et al. “Frozen-Dough Baking Potential of Psychrotolerant Saccharomyces Species and Derived Hybrids”. Food Microbiology 94 (2021): 103640.
  8. Nikulin J., et al. “Alternative Saccharomyces Interspecies Hybrid Combinations and Their Potential for Low-Temperature Wort Fermentation”. Yeast1 (2018): 113-127.
  9. Liti G., et al. “High Quality De Novo Sequencing and Assembly of the Saccharomyces arboricolus Genome”. BMC Genomics 14 (2013): 69.
  10. Danchin A., et al. “Mapping the Bacterial Cell Architecture into the Chromosome”. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences1394 (2000): 179-190.
  11. Stauffer D and Cebrat S. “Haplotype Complementarity Under Mutational Pressure”. Frontiers in Bioscience2 (2011): 408-415.
  12. Balzano E and Giunta S. “Centromeres under Pressure: Evolutionary Innovation in Conflict with Conserved Function”. Genes8 (2020): 912.
  13. Tomasch J., et al. “Connection Between Chromosomal Location and Function of CtrA Phosphorelay Genes in Alphaproteobacteria”. Frontiers in Microbiology 12 (2021): 662907.
  14. Ling MHT., et al. “Conserved Expression of Natural Antisense Transcripts in Mammals”. BMC Genomics 14 (2013): 243.
  15. Keng BM., et al. “Codon Usage Bias is Evolutionarily Conserved”. Asia Pacific Journal of Life Sciences3 (2014): 233-242.
  16. Wang M., et al. “The Non-Random Patterns of Genetic Variation Induced by Asymmetric Somatic Hybridization in Wheat”. BMC Plant Biology1 (2018): 244.
  17. Lim GZ., et al. “Significant Differences in Nucleotide and Peptide Features Between Chromosomes Suggesting Sequence Non-randomness Across Chromosomes”. Acta Scientific Microbiology4 (2021): 23-28.
  18. Lobry JR and Gautier C. “Hydrophobicity, Expressivity and Aromaticity are the Major Trends of Amino-Acid Usage in 999 Escherichia coli Chromosome-Encoded Genes”. Nucleic Acids Research15 (1994): 3174-3180.
  19. Kyte J and Doolittle RF. “A Simple Method for Displaying the Hydropathic Character of a Protein”. Journal of Molecular Biology1 (1982): 105-132.
  20. Bjellqvist B., et al. “The Focusing Positions of Polypeptides in Immobilized pH Gradients can be Predicted from Their Amino Acid Sequences”. Electrophoresis10 (1993): 1023-1031.
  21. Guruprasad K., et al. “Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence”. Protein Engineering2 (1990): 155-161.
  22. Cock PJA., et al. “Biopython: Freely Available Python Tools for Computational Molecular Biology and Bioinformatics”. Bioinformatics11 (2009): 1422-1423.
  23. Ling MHT. “SeqProperties: A Python Command-Line Tool for Basic Sequence Analysis”. Acta Scientific Microbiology6 (2020): 103-106.
  24. Maitra A and Ling MH. “Codon Usage Bias and Peptide Properties of Pseudomonas balearica DSM 6083T”. MOJ Proteomics and Bioinformatics2 (2019): 27-39.
  25. Kim JH and Ling MH. “Proteome Diversities Among 19 Archaebacterial Species”. Acta Scientific Microbiology5 (2019): 20-27.
  26. Das B and Chattoraj DK. “Commentary: Functionality of Two Origins of Replication in Vibrio cholerae Strains with a Single Chromosome”. Frontiers in Microbiology 10 (2019): 1314.
  27. Jha JK., et al. “Chromosome Dynamics in Multichromosome Bacteria”. Biochimica Et Biophysica Acta7 (2012): 826-829.
  28. Kellis M., et al. “Proof and Evolutionary Analysis of Ancient Genome Duplication in the Yeast Saccharomyces cerevisiae”. Nature6983 (2004): 617-624.
  29. Wolfe KH and Shields DC. “Molecular Evidence for an Ancient Duplication of the Entire Yeast Genome”. Nature6643 (1997): 708-713.
  30. Wolfe KH. “Origin of the Yeast Whole-Genome Duplication”. PLoS Biology8 (2015): e1002221.
  31. Shao Y., et al. “Creating a Functional Single-Chromosome Yeast”. Nature7718 (2018): 331-335.
  32. Luo J., et al. “Karyotype Engineering by Chromosome Fusion Leads to Reproductive Isolation in Yeast”. Nature7718 (2018): 392-396.
  33. Gu X., et al. “Single-Chromosome Fission Yeast Models Reveal the Configuration Robustness of a Functional Genome”. Cell Reports8 (2022): 111237.
  34. Doughty TW., et al. “A Single Chromosome strain of cerevisiae Exhibits Diminished Ethanol Metabolism and Tolerance”. BMC Genomics 22.1 (2021): 688.
  35. Bochkareva OO., et al. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia spp”. BMC Genomics1 (2018): 965.

Maurice HT Ling., et al. “Peptide Properties of Saccharomyces arboricola H-6 Suggest Randomness in Chromosomal Organization”. EC Microbiology  19.3 (2023): 01-08.