Saccharomyces Cerevisiae- Chromosome VII

In 1996 was released the genome of the yeast Saccharomyces Cerevisiae which was the first eukaryotic organism to be sequenced. It’s composed by sixteen chromosomes and we’ll be focusing on the seventh, having the Saccharomyces Genome Database (SGD) as a reference for our research.

             The chromosome VII has a total length of 1,090,940 bp that can be separated by the   centromere (CEN7) in two arms. The left arm has 496920 bp while the right arm has 593902 bp (figure 1). There are twenty-six ARS (autonomously replicating sequences). The sequence of ARS 706 is shown below (figure 2).

Figure 1- CEN7 (https://www.yeastgenome.org/locus/S000006468)

Figure 2- ARS 706 sequence

         A lot of genes are involved in replication, such as RFC5, SLD3, MCM6, MPT5 and HFM1.

           RFC5 is a DNA binding protein and ATPase that acts as a clamp loader of the proliferating cell nuclear antigen (PCNA) processivity factor for DNA polymerase delta and epsilon.

           SLD3 is involved in the initiation of DNA replication, as well it’s required for proper assembly of replication proteins at the origins of replication.

            MCM6 is a component of the Mcm2-7 hexameric helicase complex that binds chromatin as a part of the pre-replicative complex.

            MPT5 is a mRNA-binding protein. It has broad specificity, recruits the CCR4-NOT deadenylase complex to mRNAs along with Dhh1p and Dcp1p to promote deadenylation, decapping, and decay.

            HFM1 is a meiosis specific DNA helicase. It participates in the conversion of double-stranded breaks to later recombination intermediates, in crossover control and catalyses the unwinding of Holliday junctions.

      References:

1. H Tettelin, et al,1997, The nucleotide sequence of Saccharomyces Cerevisiae chromosome VII, Nature, Volume 387, 81-83;
2. SGD: Saccharomyces Genome Database (https://www.yeastgenome.org).

           Group 2.3: Ana Vale, André Magalhães, Bárbara Alves, Maria Loureiro and Marta Caçador. Biochemistry 2^nd year (2018/2019). University of Minho.

Saccharomyces cerevisiae Chromosome VIII

The genome of Saccharomyces cerevisiae is made up of 16 chromosomes. The data presented in this document is our research on the Chromosome VIII. Chromosome VIII has a total length of 562643 bp and 385 genes. The centromere of this chromosome (FIG.1) is located between the bases 105586 and 105703 bp and contains 118 bp. The left arm has 105586 bp, while the right arm has 457 057 bp.

FIG.1 - Representative scheme of the Chromosome VIII Centromere.

From a total of 385 genes present in this chromosome (FIG.2), 321 are functional (ORF- open reading frame), which corresponds to 83,4%. Other significant percentages correspond to long terminal repeat (6,2%) and ARS - autonomously replicating sequence - (4,2%), which corresponds to 16 ARS in total, for example, ARS815 (its sequence as shown in FIG.3). There are many genes involved in replication (TAB.1)   

FIG.2 – Feature Types for Chromosome VIII

 FIG 3 - Nucleotide sequence for ARS815.

TAB 1 – Some genes in CHR VIII used for DNA Replication

Grupo 3.1
Ana Sousa, Sara Castro, Ana Luísa, Bruna Novais, Carolina Gonçalves

Licenciatura: Bioquímica

UMinho

Reference: M. Johnston, et al., 1994, Science 265:2077-82

The chromosome XII of Saccharomyces cerevisiae

The chromosome that we are studying, chromosome XII belongs to a yeast genome, Saccharomyces cerevisiae, composed by sixteen chromosomes.

This chromosome shows specific features that define him. Is formed by 1078177 bp, the longer arm measures 92053 bp and the shorter has a length of 150820 bp. It has about 534 functional genes (ORF’S) and from these genes, some are involved in replication, such as: TEN1, MEC3, EST2, SLX4, IFH1. The first one, TEN1, it’s a protein that regulates telomeric length. MEC3 it’s responsible of doing the checkpoint of the DNA damage and meiotic pachytene (one of the five subphases of prophase I) and it’s also a subunit of a heterometric complex that forms a sliding clamp (the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand). The gene EST2 is the reverse transcriptase subunit of the telomerase holoenzyme. SLX4 it’s an endonuclease involved in DNA processing in addition to acting during recombination and repair. The last one we refereed, the gene IFH1 it´s a coactivator and regulates transcription of ribosomal protein (RP) genes.

We researched that chromosome XII has a total of 29 autonomously replicating sequences (ARS) within:  ARS 1202, ARS 1206, ARS1207, ARS1208 (figure 1), ARS1209, ARS1210, ARS1211, ARS1212, ARS1212.5, ARS1213, ARS1214, ARS1215, ARS1216, ARS1200-1, ARS1200-2, ARS1217, ARS1218, ARS1219, ARS1220, ARS1221, ARS1223, ARS1226, ARS1238, ARS 1228, ARS1230, ARS1232, ARS1233, ARS 1234, ARS1235, that mark the initiation of replication.

Figure 1- Sequence of ARS 1208 

https://browse.yeastgenome.org/?loc=chrXII%3A24001..178800&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CDoube_strand_break_hotspots%2CXrn1-sensitive_unstable%20transcripts_XUTs%2CScGlycerolMedia%2C3%27UTRs%2CPolII_occupancy_WT&highlight=

References

·      M. Johnston et al., 1997,  The nucleotide sequence of chromosome XII, NATURE, volume 387: pages 87 to 90

·      Saccharomyces genome database consulted in  29/10/2018 at https://www.yeastgenome.org/

                                                                                                                              

                                                                                                                                  Grupo 4.2

Ana Catarina Ribeiro

Catarina Faria

Fabiana Marques

Tânia Pontes 

Licenciatura em Bioquímica

Yeast Chromosome III

Yeast Chromosome III

The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. According to Oliver et al., “this is the first complete sequence analysis of an entire chromosome from any organism”.

Chromosome III is the third smallest chromosome in S. cerevisiae, the sequence is 316,620 kilobases long, the left arm contains 114,385 kilobases and the right arm contains 202,119 kilobases. This sequence reveals 198 genes of which 184 are open reading frames (ORF), 10 are tRNA genes and 4 are snoRNA genes. This chromosome contains 19 autonomously replicating sequences (ARS), such as ARS310 (fig. 1), and several genes involved in replication, for example RIM1, DCC1, MRC1, RDS1.

Nucleotide sequence of ARS310: 

Figura 1- Nucleotide sequence of ARS310

Reference:

Oliver et al., 1992, The complete DNA sequence of yeast chromosome III, Nature, vol. 357: 38-46.

Grupo 1.3 

Ana Filipa Alves de Araújo A85195

Cristiana Filipa Leite Oliveira A85237

Filipa Leal Silva A84224

Inês Mesquita Ferreira A85289

Licenciatura em Bioquímica

UMINHO

 

Saccharomyces Cerevisiae Chromosome IV

Saccharomyces cerevisiae Chromosome IV

The Saccharomyces cerevisiae chromosome IV is the longest of them all containing 1,531,974 base pairs and around 796 predicted and knowned genes having a lenght of 1531933bp (without the centromere).

Arms lenght:

·      Left arm- 449711bp

·      Right arm- 1082112bp

The average combination of G+C is 37.9% being lower than chromossome III (38.5%) and II (38.3%).

At the centromere (coordinates 500,000 to 1,215,000) there is a lower amount of G+C (37.4%) than the periferic regions (38.2%).

There are exactly 35 ARS (autonomously replicating sequences), apart from the total we take has an example ARS442. It’s sequence is the following:

From the genes involved in replication of the fourth chromosome we give special attention:

·      PSF1 / YDR013W

·      SLD5 / YDR489W

·      FOB1 / YDR110W

·      RAD30 / YDR419W

·      RAD55 / YDR076W

Cristiano Viães A84165 

Diogo Cachetas A83854 

Diogo Pinto A85142 

Sérgio Mendes A83835