Mini-review of the genome and proteome of archaea Saccharolobus shibatae B12

Elena Neverova-Simchit¹

¹Faculty of Bioengineering and Bioinformatics, 1-73, MSU, Leninskiye Gory, GSP-1, Moscow, 119991; budbe3dzgwdo@mail.ru

Abstract: What can you learn from a single prokaryote using only computational methods and results of previous studies? You will see by the end of this mini-review. We had chosen an archaea species Saccharolobus shibatae B12 to study its genome and proteome. All materials we had either found on open internet resources, either received them through modifying data collected from the former source. We worked with Python, Google Sheets, Bash and even notebooks. In the end most of our results had been achieved before us, so it can be safely said that we confirm previously received information. In this mini-review I would point out the finding of correlation between the maximum GC-content in the genome sequence and the gene product in that section. Other characteristics of the genome and proteome were also studied. Results, where convenient, are presented in visual forms.

Keywords:archaea; genome; proteome; GC-content.

1. Introduction

  Saccharolobus shibatae, an archaeal species belonging to the phylum Thermoproteota, was described for the first time as Sulfolobus shibatae in 1990, after being isolated from geothermal pools in Beppu, Japan. The isolate B12 and its endogenous virus-like element SSV1 have provided a system for detailed analysis (Grogan et al., 1990). Like all members of Sulfobaceae isolated so far this organism is a thermoacidophile adapted to low pH environments and high temperatures (Albers et al., 2014). S. shibatae can grow in complex organic compounds and in sugars, it is either a heterotrophic or mixotrophic archaeon (Grogan et al., 1990). It was transferred from the genus Sulfolobus to the new genus Saccharolobus in 2018 (Sakai, Kurosawa, 2018). The archaea genome was studied in research dedicated to reverse gyrases and their association with type I-5′ DNA topoisomerase family (Jaxel et al., 1996).
  In this review the proteome and genome of archaea Saccharolobus shibatae B12 is studied, results are analyzed, discussed from the points of previous studies and conclusions are made based on the received results.

2. Materials and Methods

  Materials used to conduct research include files received from National Centre of Biotechnological information S1 containing data about genome DNA sequences of S. shibatae S2, genome feature table S3 and table of feature counts S4, GenBank file S7. S5 contain programs written in Python: programs 1 for DNA molecule composition and GC-content. S6 contain 4 figures in which plots of guanine, cytosine and GC-content distribution are presented. S8 contains lines extracted from GenBank S7 that were used for GC-content analysis. Histogram of protein lengths is presented in sheet “Histogram” S9, number of proteins encoded in each of the DNA strands, statistical significance and relevant figures are presented in sheet “Randomness” S9, statistical information for encoded in gene proteins can be found in sheet “Statistics” S9, sheet “CDS” was used as a data base formed from feature table S3. Table of proteome analysis S10 shows lists of all, ribosomal, hypothetical, transporter proteins on respective sheets, all data can be found in sheet “CDS” formed from feature table S3, sheet “Protein Analyse” contains amounts of mentioned above proteins and relevant figures. Table of RNA analysis contains data on this subject excluded from feature table S3, information about all RNA, rRNA, tRNA genes is stored in respected sheets, the sheet “Analysis” is devoted to comparing amounts of each group of these genes. Table of gene distribution S12 contains similarly named sheets devoted to all genes, genes on the forward and reverse strands and sheet “Analysis” where comparison results can be seen.
  Methods include use of Google Sheets for data display and functions available in the program, a high-level programming language Python. Google Sheets were used in proteome analysis for building histograms, calculating statistical information, including statistical significance of distribution of product lengths and genes on DNA strands, finding amounts of certain protein types and RNA gene types. Search function of notepad was used when analyzing GC-content using GenBank S7. Unix shell and command language Bash was used to determine amount and names of separate DNA molecules in the genome from fasta file S2, the length of the longest gene products from feature table S3. Python was used in GC-content study and consists of 2 program blocks, the first one of them dividing into sections for general DNA research, GC-content analysis and plot building and the search of maximum and minimum points, the second program block is devoted towards the nucleotide frequency calculation, data from fasta file S2 was used.

3. Results

3.1.Standard information

  The genome of Saccharolobus shibatae B12 consists of two ring DNA molecules: chromosome and plasmid pB12E5. The chromosome consists of much more base pairs than the plasmid, which is a typical situation for living organisms (see Table 1). Genome size of the prokaryote, being approximately 2.9 Mb, is higher than the general of 1.6 Mb for archaea. Such genome size fits the range of genome sizes (2.47–2.85 Mb) for the genus Sulfolobus (Nicholas et al., 2018).
  The amounts of coding sequences on both DNA strands were compared, sheet “Analysis” table of gene distribution S12. The number of genes on the forward strand was only slightly bigger than that of genes on the reverse strand and statistical significance showed that such differences do not go beyond the norm.

Table 1. S. shibatae DNA length and GC structure.

DNA molecule	b.p.	GC-content
Chromosome	2879035	35.3594%
Plasmid pB12E5	37840	35.5946%
Total	2916875	35.3624%

  The number and frequency of all four nucleotides on the forward DNA strands were calculated (program 2 S5) and are presented in Table 2. It can be seen that the overall amounts of adenine and thymine are nearly equal to each other, along with the approximate equality of guanine and thymine numbers. The GC-content (guanine-cytosine content) for each DNA molecule has also been calculated (program 1 S5,) the results are presented in Table 1. In this case overall GC-content is not very large.

Table 2. S. shibatae nucleotide frequency in the forward DNA strands.

Nucleotide	Chromosome	Plasmid pB12E5	Total
A	32.47%	31.97%	32.46%
T	32.17%	32.43%	32.18%
G	17.85%	18.19%	17.85%
C	17.51%	17.41%	17.51%

3.2. More about GC-content

  GC-content was then analyzed on DNA sections. The results are presented in Table 3, Figure 1 and plots S6. As can be seen from Figure 1 GC-content varies in a sufficient but not too large range and changes in a jumpy way from section to section. The maximum and minimum points were calculated and products coded in these regions were found using notebook S8, see Table 3 for results. The highest GC content for the chromosome is presented in an rRNA coding part of the DNA strand. It is also noticeable that GC-content in the chromosome is higher in a gene that has a definite product. In the plasmid GC-content is lower in a non-coding region of the DNA, than in the one responsible for protein coding.

Table 3. The maximum and minimum points of S. shibatae GC structure (window 1000, step 1000 for chromosome; window 100, step 1000 for plasmid).

Type of information	Chromosome	Plasmid pB12E5
Maximum GC-content	63.00%	44.00%
Approximate max location	2268000	18500
Product	rRNA	Hypothetical protein
Minimum GC-content	23.70%	28.10%
Approximate min location	1403000	27400
Product	Hypothetical protein	None