Wednesday, 6 July 2016

SMBE2016: Investigating the evolution of new biochemical pathways in baker’s yeast Saccharomyces cerevisiae

Well done to Åsa for her oral presentation at SMBE2016 (#204):

Investigating the evolution of new biochemical pathways in baker’s yeast Saccharomyces cerevisiae

Åsa Pérez-Bercoff, Tonia L. Russell, Philip J. L. Bell, Paul V. Attfield & Richard J. Edwards

Abstract

Understanding how new biochemical pathways evolve in a sexually reproducing population is a complex and largely unanswered question. We have successfully evolved a novel biochemical pathway in yeast using a sex based population approach.

For over 30 years, wild type Saccharomyces has been widely reported to not grow on xylose at all, but we discovered that most strains can grow, albeit at almost undetectable rates. A mass mated starting population of Saccharomyces cerevisiae strains was evolved under selection on Xylose Minimal Media (XMM) with forced sexual mating every ~two months for 1463 days. This produced a population that could grow on xylose as a sole carbon source. Initial studies show the xylose growth trait is quantitative and presumably governed by many genes. To investigate the evolution of the xylose phenotype, a xylose utilising strain MBG11a was isolated. MBG11a was sequenced with PacBio RSII long read sequencing at the Ramaciotti Centre for Genomics. A high quality complete genome was assembled de novo using the hierarchical genome-assembly process (HGAP3) using only PacBio non-hybrid long-read SMRT sequencing data, corrected using Quiver, and compared to the genome of the S. cerevisiae S288C reference genome.

Approximately 98.5% of the MBG11a genome could be aligned to S288C at 99.5% sequence identity, with over 15,000 non-synonymous and 200 nonsense SNP differences. We have crossed MBG11a with a reference wild type yeast strain (X2180 gal2, Xyl-) and are testing offspring on different minimal media in an attempt to identify MBG11a variants responsible for the novel growth phenotype.

Understanding what has occurred in the evolving yeast population, and how the yeast genome adapted under the selection pressures is of broad interest as it allows experimental analysis of how novel complex biological functions can evolve in an organism.

Monday, 20 June 2016

Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome

Lin P, Nicholls L, Assareh H, Fang Z, Amos TG, Edwards RJ, Assareh AA, Voineagu I (2016): Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome. BMC Genomics 17(1):427. doi: 10.1186/s12864-016-2746-7.

Abstract

BACKGROUND: MECP2, the gene mutated in the majority of Rett syndrome cases, is a transcriptional regulator that can activate or repress transcription. Although the transcription regulatory function of MECP2 has been known for over a decade, it remains unclear how transcriptional dysregulation leads to the neurodevelopmental disorder. Notably, little convergence was previously observed between the genes abnormally expressed in the brain of Rett syndrome mouse models and those identified in human studies.

METHODS: Here we carried out a comprehensive transcriptome analysis of human brain tissue from Rett syndrome brain using both RNA-seq and microarrays.

RESULTS: We identified over two hundred differentially expressed genes, and identified the complement C1Q complex genes (C1QA, C1QB and C1QC) as a point of convergence between gene expression changes in human and mouse Rett syndrome brain.

CONCLUSIONS: The results of our study support a role for alterations in the expression level of C1Q complex genes in RTT pathogenesis.

PMID: 27267200

Thursday, 26 May 2016

Honours applications close next Friday (3 June)

We still have space in the group for one more Honours student, with a variety of projects available to work on PacBio SMRT data for bacteria, yeast or cane toad de novo genome assembly. Please get in touch if you are interested. (Better still, fill in the lab application form, making it clear it’s for Honours, not PhD!) The deadline is Friday, 3rd of June. See the BABS website for more details.

Thursday, 12 May 2016

Congratulations, Dr Joe Jenkins!

Congratulations to Joe Jenkins, who successfully defended his PhD on 12th May and was awarded his doctorate following his viva, with Professor Gary Bending as external examiner. It’s been a busy week for Joe, with the main paper from his PhD out this week too!

Tuesday, 10 May 2016

Biochar alters the soil microbiome and soil function: results of next generation amplicon sequencing across Europe

Jenkins JR, Viger M, Arnold EC, Harris ZM, Ventura M, Miglietta F, Girardin C, Edwards RJ, Rumpel C, Fornasier F, Zavalloni C, Tonon G, Alberti G & Taylor G (2016): Biochar alters the soil microbiome and soil function: results of next generation amplicon sequencing across Europe. GCB Bioenergy Adv. Access DOI: 10.1111/gcbb.12371

Abstract

Wide scale application of biochar to soil has been suggested as a mechanism to offset increases in CO2 emissions through the long-term sequestration of a carbon rich and inert substance to the soil, but the implications of this for soil diversity and function remain to be determined. Biochar is capable of inducing changes in soil bacterial communities, but the exact impacts of its application are poorly understood. Using three European sites (UK SRC, short rotation coppice, French grassland (FR) and Italian SRF, short rotation forestry (IT)) treated with identical biochar applications; we undertook 16S and ITS amplicon DNA sequencing. In addition, we carried out assessments of community change over time and N and P mobilisation in the UK.

Significant changes in bacterial and community structure occurred due to treatment, although the nature of the changes varied by site. STAMP differential abundance analysis showed enrichment of Gemmatimonadete and Acidobacteria in UK biochar plots one year after application, whilst control plots exhibited enriched Gemmataceae, Isosphaeraceae and Koribacteraceae. Increased mobility of ammonium and phosphates were also detected after one year, coupled with a shift from acid to alkaline phophomonoesterase activity, which may suggest an ecological and functional shift towards a more copiotrophic ecology. Italy also exhibited enrichments, in both the Proteobacteria (driven by an increase in the order Rhizobiales) and the Gemmatimonadetes. No significant change in the abundance of individual taxa were noted in FR, although a small significant change in unweighted UNIFRAC occurred, indicating variation in the identities of taxa present due to treatment. Fungal β diversity was affected by treatment in IT and FR, but was unaffected in UK samples. The effects of time and site were greater than that of biochar application in UK samples. Overall, this report gives a tantalising view of the soil microbiome at several sites across Europe, and suggests that although application of biochar has significant effects on microbial communities, these may be small compared with the highly variable soil microbiome that is found in different soils and changes with time.

Friday, 6 May 2016

ARC Linkage Success! - Elucidating the genetic basis of newly evolved metabolic functions in yeast

We are very happy to report a successful ARC Linkage Projects 2016 grant application:

LP160100610: Elucidating the genetic basis of newly evolved metabolic functions in yeast

Dr Richard Edwards; Professor Marc Wilkins; Associate Professor Mark Tanaka; Dr Paul Attfield; Dr Phillip Bell

This project intends to research how complex metabolic pathways originate and evolve. This project will use cutting edge genome sequencing and molecular techniques to elucidate the heritable genetic basis of Baker’s yeast, which has been the selectively evolved to use xylose as a sole carbon source: something vital for second generation biofuel production that wild yeast cannot do. This project will combine detailed molecular characterisation of highly adapted yeast strains with a novel “molecular palaeontology” approach to trace the evolutionary process and identify functionally significant loci under selection. Detailed characterisation of this trait will accelerate the development of future yeast strains and test fundamental evolutionary theories.

This will continue the work we have been doing on PacBio sequencing and yeast genomics in collaboration with our industrial partners, Microbiogen Pty Ltd.

There will be job and studentship opportunities associated with this grant, so watch this space! (Or get in touch!)